A modular tool to aggregate results from bioinformatics analyses across many samples into a single report.
This report has been generated by the nf-core/funcscan analysis pipeline. For information about how to interpret these results, please see the documentation.
/home/yasemen/School/BacterialGenomics/nf-corePipelines/funcscan/work/33/703d3d157eec5db05e1adcd95cd5bf
Software Versions
Software Versions lists versions of software tools extracted from file contents.
| Group | Software | Version |
|---|---|---|
| ABRICATE_RUN | abricate | 1.0.1 |
| AMPCOMBI2_CLUSTER | ampcombi | 2.0.1 |
| AMPCOMBI2_COMPLETE | ampcombi | 2.0.1 |
| AMPCOMBI2_PARSETABLES | ampcombi | 2.0.1 |
| AMPIR | ampir | 1.1.0 |
| AMPLIFY_PREDICT | AMPlify | 2.0.0 |
| AMP_DATABASE_DOWNLOAD | ampcombi | 2.0.1 |
| AMRFINDERPLUS_RUN | amrfinderplus | 4.0.23 |
| amrfinderplus-database | null | |
| AMRFINDERPLUS_UPDATE | amrfinderplus | 4.0.23 |
| ANTISMASH_ANTISMASH | antismash | 8.0.1 |
| ANTISMASH_ANTISMASHDOWNLOADDATABASES | antismash | 8.0.1 |
| ARGNORM_ABRICATE | argnorm | 0.5.0 |
| ARGNORM_DEEPARG | argnorm | 0.5.0 |
| COMBGC | comBGC | null |
| DEEPARG_DOWNLOADDATA | deeparg | 1.0.4 |
| DEEPARG_PREDICT | deeparg | 1.0.4 |
| DEEPBGC_DOWNLOAD | deepbgc | 0.1.31 |
| DEEPBGC_PIPELINE | deepbgc | 0.1.31 |
| prodigal | 2.6.3 | |
| FARGENE | fargene | 0.1 |
| GECCO_RUN | gecco | 0.9.10 |
| GUNZIP_MACREL_ORFS | gunzip | 1.13 |
| GUNZIP_MACREL_PRED | gunzip | 1.13 |
| GUNZIP_PYRODIGAL_FAA | gunzip | 1.13 |
| GUNZIP_PYRODIGAL_FNA | gunzip | 1.13 |
| GUNZIP_PYRODIGAL_GBK | gunzip | 1.13 |
| HAMRONIZATION_ABRICATE | hamronization | 1.1.9 |
| HAMRONIZATION_AMRFINDERPLUS | hamronization | 1.1.9 |
| HAMRONIZATION_DEEPARG | hamronization | 1.1.9 |
| HAMRONIZATION_RGI | hamronization | 1.1.9 |
| HAMRONIZATION_SUMMARIZE | hamronization | 1.1.9 |
| MACREL_CONTIGS | macrel | 1.4.0 |
| PYRODIGAL | pyrodigal | 3.6.3 |
| RGI_CARDANNOTATION | rgi | 6.0.5 |
| rgi-database | 4.0.1 | |
| RGI_MAIN | rgi | 6.0.5 |
| rgi-database | 4.0.1 | |
| SEQKIT_SEQ_LENGTH | seqkit | v2.9.0 |
| UNTAR_CARD | untar | 1.34 |
| Workflow | Nextflow | 25.10.0 |
| nf-core/funcscan | v3.0.0-gfa9db01 |
nf-core/funcscan Methods Description
Suggested text and references to use when describing pipeline usage within the methods section of a publication.URL: https://github.com/nf-core/funcscan
Methods
Data was processed using nf-core/funcscan v3.0.0 (doi: 10.5281/zenodo.7643099) of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
The pipeline was executed with Nextflow v25.10.0 (Di Tommaso et al., 2017) with the following command:
nextflow run nf-core/funcscan -profile docker --input samplesheet.csv --outdir runscanResults --run_amp_screening --run_arg_screening --run_bgc_screening -c ./funcscan.config
Th.ipelin.se.h.ollowin.ools.reprocessin.nclude.eqKit.She..l.024).nnotatio.a.arrie.u.ith.Pyrodiga.Larrald.022).h.ollowin.ntimicrobia.eptid.creenin.ool.er.sed.MPlif.L..l.022).acre.Santos-Júnio..l.020).mpi.Fingerhu..l.021)..h.utpu.ro.h.ntimicrobia.eptid.creenin.ool.er.tandardise.n.ummarise.it.MPcomb.Ibrahi.n.erel.023).h.ollowin.ntimicrobia.esistanc.en.creenin.ool.er.sed.ARGen.Berglun..l.019).G.Alcoc..l.020).MRfinderplu.Feldgarde..l.021).eepAR.Arango-Argot.018).BRicat.Seeman.020).h.utput.ro.R.creenin.ool.er.ormalize..h.ntibioti.esistanc.ntolog.sin.rgNor.Ugarcin.erovi..l.025).h.utpu.ro.h.ntimicrobia.esistanc.en.creenin.ool.er.tandardise.n.ummarise.it.AMRonizatio.Maguir..l.023).h.ollowin.iosyntheti.en.luste.creenin.ool.er.sed.ntiSMAS.Bli..l.021).eepBG.Hanniga..l.019).ECC.Carrol..l.021).h.utpu.ro.h.iosyntheti.en.luste.creenin.ool.er.tandardise.n.ummarise.it.omBG.Frangenber..l.023).u.tatistic.er.eporte.sin.ultiQ.Ewel..l.016).
References
- Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
- Shen, W., Sipos, B., & Zhao, L. (2024). SeqKit2: A Swiss army knife for sequence and alignment processing. iMeta, e191. https://doi.org/10.1002/imt2.191
- Larralde, M. (2022). Pyrodigal: Python bindings and interface to Prodigal, an efficient method for gene prediction in prokaryotes. Journal of Open Source Software, 7(72), 4296. DOI: 10.21105/joss.04296
- Li...utherland...ammond.. A..ang...aho...ergman...ouston...arren.. L..ong...oang...ameron.. E..elbing.. C.. Birol.. (2022). AMPlify: attentive deep learning model for discovery of novel antimicrobial peptides effective against WHO priority pathogens. BMC genomics.3(1).7. DOI: 10.1186/s12864-022-08310-4
- Santos-Júnior.. D..an...hao.. M.. Coelho.. P. (2020). Macrel: antimicrobial peptide screening in genomes and metagenomes. PeerJ..10555. DOI: 10.7717/peerj.10555
- Fingerhut...iller.. J..trugnell.. M..aly.. L.. Cooke.. R. (2021). ampir: an R package for fast genome-wide prediction of antimicrobial peptides. Bioinformatics (Oxford.ngland).6(21).262–5263. DOI: 10.1093/bioinformatics/btaa653
- Ibrahim.. & Perelo.. (2023). Darcy220606/AMPcombi. DOI: 10.5281/zenodo.7639121
- Berglund...sterlund...oulund...arathe.. P..arsson... Kristiansson.. (2019). Identification and reconstruction of novel antibiotic resistance genes from metagenomes. Microbiome.(1).2. DOI: 10.1186/s40168-019-0670-1
- Alcock.. P..aphenya.. R..au...sang.. K..ouchard...dalatmand...uynh...guyen.. V..heng.. A..iu...in.. Y..iroshnichenko...ran.. K..erfalli.. E..asir.. A..loni...peicher.. J..lorescu...ingh...altyn... McArthur.. G. (2020). CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic acids research.8(D1).517–D525. DOI: 10.1093/nar/gkz935
- Feldgarden...rover...onzalez-Escalona...rye.. G..aendiges...aft.. H..offmann...ettengill.. B..rasad.. B..illman.. E..yson.. H.. Klimke.. (2021). AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance.tress response.nd virulence. Scientific reports.1(1).2728. DOI: 10.1038/s41598-021-91456-0
- Arango-Argoty...arner...ruden...eath.. S..ikesland... Zhang.. (2018). DeepARG: a deep learning approach for predicting antibiotic resistance genes from metagenomic data. Microbiome.(1).3. DOI: 10.1186/s40168-018-0401-z
- Seemann.. (2020). ABRicate. Github https://github.com/tseemann/abricate.
- Ugarcina Perovic...amji...hong...uan...aguire...oelho.. P. (2025). argNorm: normalization of antibiotic resistance gene annotations to the Antibiotic Resistance Ontology (ARO).ioinformatics.taf173. DOI: 10.1093/bioinformatics/btaf173
- Public Health Alliance for Genomic Epidemiology (pha4ge). (2022). Parse multiple Antimicrobial Resistance Analysis Reports into a common data structure. Github. Retrieved October 5.022.rom https://github.com/pha4ge/hAMRonization
- Blin...haw...ader...zenei...eitz..L..ugustijn..E..ediel-Becerra..D.D..e Crécy-Lagard...oetsier..A..illiams..E..ruz-Morales...ongwas...egurado Luchsinger..E..iermann...orenskaia...douc..M..eijer...erlouw..R..an der Hooft..J.J..iemert...elfrich..J.N..asschelein...orre...hevrette..G..an Wezel..P..edema..H..eber...025. antiSMASH 8.0: extended gene cluster detection capabilities and analyses of chemistry.nzymology.nd regulation. Nucleic Acids Res. 53.32-W38. DOI: 10.1093/nar/gkz654
- Carroll.. M. .arralde...leck.. S..onnudurai...ilanese...appio Barazzone.. & Zeller.. (2021). Accurate de novo identification of biosynthetic gene clusters with GECCO. bioRxiv DOI: 0.1101/2021.05.03.442509
- Frangenberg.. Fellows Yates.. A..brahim...erelo... Beber.. E. (2023). nf-core/funcscan: 1.0.0 - German Rollmops - 2023-02-15. https://doi.org/10.5281/zenodo.7643100
- Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics , 32(19), 3047–3048. https://doi.org/10.1093/bioinformatics/btw354
Notes:
- The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
nf-core/funcscan Workflow Summary
- this information is collected when the pipeline is started.URL: https://github.com/nf-core/funcscan
Input/output options
- input
- samplesheet.csv
- outdir
- runscanResults
Screening type activation
- run_amp_screening
- true
- run_arg_screening
- true
- run_bgc_screening
- true
AMP: ampcombi2 parsetables
- amp_ampcombi_parsetables_dbevalue
- 5
AMP: ampcombi2 cluster
- amp_ampcombi_cluster_covmode
- 0
- amp_ampcombi_cluster_mode
- 1
ARG: AMRFinderPlus
- arg_amrfinderplus_identmin
- -1
Generic options
- trace_report_suffix
- 2025-12-19_10-55-14
Core Nextflow options
- configFiles
- /home/yasemen/.nextflow/assets/nf-core/funcscan/nextflow.config, /home/yasemen/School/BacterialGenomics/nf-corePipelines/funcscan/./funcscan.config
- containerEngine
- docker
- launchDir
- /home/yasemen/School/BacterialGenomics/nf-corePipelines/funcscan
- profile
- docker
- projectDir
- /home/yasemen/.nextflow/assets/nf-core/funcscan
- revision
- master
- runName
- spontaneous_mccarthy
- userName
- yasemen
- workDir
- /home/yasemen/School/BacterialGenomics/nf-corePipelines/funcscan/work